I'm not exactly sure what you're asking for, but all side quests are in their own time bubble. It's why you can complete EW but then go do the Drg quests where you meet Estinien for the first time. Or back during 2.55 people could go and do the lv 50 Cul quest and have a Nanamo who wasn't dead as that's what people thought back then. The game for the most part figures you'll have gone and done all the non MSQ stuff at some point. This included the Crystal Tower until 5.3 and the Devs felt it was too important to allow people to not have done it before reaching the Trial in 5.3.